biology essay

The Reactions Of Arynes Biology Essay

Published: 23, March 2015

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In chemistry, an aryne is an uncharged reactive intermediate compound derived from an aromatic system by removal of two adjacent hydrogen atoms from, respectively, an aromatic ring or a heterocyclic aromatic ring, leaving two orbitals with two electrons distributed between them.

1.2 Reactions of Arynes25:

Arynes are extraordinary reactive even at low temperature. Their reactions can be divided into three groups.

Pericyclic reactions of arynes

Nucleophilic additions to arynes

The transition metal-catalysed reactions of arynes

Pericyclic reactions of arynes:

The pericyclic reactions can be divided into some categories such as the Diels-Alder reactions (cycloaddition reaction); the [2+2] cycloadditions; the 1-3-dipolar cycloadditions; the 1-4-dipolar cycloadditions and the ene reactions. In cycloaddition reaction two or more unsaturated molecules (or parts of the same molecule) combine with the formation of a cyclic adduct.

Reaction 1: Cycloaddition reaction.

In the above example aryne intermediates are generated and then undergo further reaction.

Nucleophilic additions to arynes25:

The arynes react with particularly all kind of nucloephiles, from a synthetic point of view, the most interesting are the nitrogen containing nucleophiles and carbanions. The addition of nucleophiles to arynes is highly regioselective when the position adjacent to the triple bond having electron-withdrawing group (EWG). Nucleophilic reaction that requires at least one substituent which is strongly electron withdrawing by resonance to become stable the anionic addition intermediate.

A halide can treated with a strong base such as amide, to remove o- aromatic proton and produce benzyne, the use of strong base which may act as nucleophiles.

Reaction 2: Nucleophilic addition reaction.

In the above reaction chlorobenzene, having an isotopic labelled carbon atoms gives substitution product (aminobenzene-labelled carbon jumbled between two isotopes) and the reaction proceeds through a symmetrical intermediate benzyne, in which equal amounts of amino benzenes with the 14C at C-1 and C-2 would be formed via attack at either end of the .

1.3 Use of arynes in organic synthesis1, 2, 25:

The importance of arynes, is used for synthesis of natural products particularly alkaloids.

Synthesis of ellipticene, an anti-cancer alkaloid

Synthesis of an aporphine alkaloid

Synthesis of a lysergic acid diethylamide

1.4 History of Benzyne5,12:

Benzyne is an example of an example of aryne with a triple bond, any derivative of benzene formally produced by abstraction of two hydrogen atoms, especially one produced by abstraction from neighbouring atoms to produce a formal triple bond. This is not a triple bond as the second pi (π) interaction results from a weak interaction of sp2 hybrid orbitals lying in the plane of ring.

Structure12 1: Benzyne.

The simplest aryne, C6H4 (dihydrobenzene), is known as benzyne. Structural representation for benzyne is, like benzene, structure 1 and 2 stabilized by resonance so like the case of benzene, a better electron structure would be 3. Benzyne is strained and highly reactive compound. Benzyne is an extremely reactive species due to the nature of its triple bond. Cyclopentadiene is a suitable chemical trap for benzyne.

1.5 Structure and Reactivity of benzyne5, 25:

In 1953 Robert's classic experiments on the conversion of 14C-labelled chlorobenzene with potassium amide to aniline gave strong o-benzyne. Additional evidence for the existence of o-benzyne was provided by the observation of its IR Spectrum,25 solid-state 13C NMR Spectrum.25

C:\Users\sagar\Desktop\benzyneep.jpg

Figure : Benzyne

Available from: http://www.chem.ucalgary.ca/courses/351/carey/ch23/ch23-3-4.html.

The image represents the benzyne electrostatic potential, low and high electron density. Here we see the triple bond (benzyne) as a region of high electron density. As a result of the non-linear triple bond, benzyne is highly reactive compound. Benzyne is active intermediate, and tends to undergo addition reactions.

1.6 Elimination-addition reactions of benzyne5:

Because of unstable triple bond in benzyne makes it reactive towards addition reaction.

Reaction 3: Elimination-addition reaction.

In the above mechanism benzyne can be derived from chlrobenzene but this reaction needs a strong base such KNH2.This reaction undergo elimination and then addition.

Reaction 4: Elimination-addition reaction.

Elimination - addition mechanism: Benzyne5:

This reaction is followed when the nucleophile is strong base for example amide ion, NH2-

Reaction 5: Elimination reaction mechanism.

Reaction 6: Addition reaction mechanism.

Mechanism of the addition of ammonia to benzyne5:

Step1:- The N in amide acts as the nucleophile and attacks the reactive triple bond C in benzyne creating a new C-N bond and an intermediate carbon ion.

Step2:- Rapid protonation of the reactive carbon ion from the ammonia forms the aniline and another molecule of the amide ion.

Reaction 7: Ammonia to Benzyne mechanism reaction.

1.7 Benzyne structure existence6,7, 8, 9, 10, 11:

Aromatic biradicals of benzyne three isomers have been the subjects of many theoretical and experimental studies. O-benzyne was discovered by Robert's classic experiment in 1956 as a reactive intermediate in the nucleophilic substitution of halo benzenes, m-benzyne was discovered by Wasburns while trapping and benzyne was discovered later.

1.8 Diels-Alder reaction13, 14, 15, 25:

The Diels-Alder reaction was discovered by Otto Diels and Kurt Alder in 1928. This reaction considered to be one of the famous and important reactions found in organic chemistry, and is often used for the synthesis of six-membered rings. In the Diels-Alder reaction, three π bonds, two in a diene and one in a dienophile, reorganise to give a six-membered ring containing one- π bond and two new sigma bonds.

One of the most important and useful reactions of benzyne is the Diels-Alder reactions with conjugated dienes, here is a simple example.

Reaction 8: Diels-Alder reaction.

Diels-Alder reaction mechanism14:

In fact, the exact Diels-Alder mechanism was unknown, However, the researchers revealed three main ideas, based on the following three studies.

The mechanism is determined and synchronous.

The mechanism is determined and synchronous

The mechanism is stepwise, first with formation of single bond and then followed by a faster formation of second bond.

Benzyne formation and the stepwise decomposition of benzenediazonium-2-carboxylate16:

The diazotisation of anthranilic acid and its derivatives is a common method to produce benzyne and its substituted benzynes after loss of nitrogen and carbon dioxide from neutral diazonium salt. Benzene diazonium-2-carboxylate may be produced in situ from anthranilic acid by diazotisation in an aprotic medium (isoamyl nitrate in 2, 2-dimethoxy ethane as a solvent), or by the removal of the elements of hydrogen chloride from 2-carboxybenzenediazonium chloride.

Reaction 9: Decomposition of benzyne.

Thus by following the above procedure benzyne can be trapping with number of dienes such as cyclopentadiene, 1, 3-diphenylisobenzofuran, 2-pyrone.

2.0 Instrumentation:

2.1 Infrared spectroscopy18,17,23 (IR):

IR is one of the classical methods for structure determination of small molecules, which can be used to identify molecules by analysis of vibration stretching frequencies for a molecule must cause a net change in the dipole moment of the molecule. The alternative electrical field of the radiation interacts with functions in the dipole moment of molecule. If the frequency of the radiation equal to vibration frequency of the molecule then the radiation will be absorbed causing a change in the amplitude of molecule vibration. The usual range of an infrared spectrum is there, between 4000 cm-1 at the high frequency end and 625 cm-1 at the low frequency end. IR spectroscopy can be used in the quantitative measurement of the sample by applying Beer-Lambert Law.

Compound was crushed in a mortar to make a fine powder and mix further with nujol to make slurry. Substance was rubbed on glass disc and placed in a chamber for analysis.

2.2 Gas chromatography-Mass spectroscopy17,19,23 (GC-MS):

GC-MS is an analytical method used for separation and identification of small molecules in a sample mixture. The GC-MS instrument consists of two parts. Gas chromatography separate volatile and semi volatile compounds based on their thermal stability, but it cannot identify them. Mass spectrometry can provide detailed structure information.

2 mg of substance was dissolved in 10 ml of acetone and filled in a labelled vial and placed in the instrument for analysis. Mass spectra were recorded using a Varian CP-3800, Gas chromatography Varian 1200L Quadrupole mass spectrometer.

2.3 Nuclear magnetic resonance spectrometry17,23 (NMR):

NMR is a technique using for identification and structural analysis of organic compounds. It involves transition of a nucleus from one spin state to another with the resultant absorption of EMR by spin active when they are place in a magnetic field. NMR pertains to nuclei and only one type nucleus at a time (Eg.1H or 13C or 19F nuclei). A plot of peak intensities versus the frequencies of absorption (expressed in δ) constitutes an NMR spectrum.

2mg of sample was taken in to a vial and dissolved it in CDCl3 using sonicator. One percentage of tetramethyl silane (TMS) was added and made the volume up to 5cm of filtered sample in a NMR tube. All NMR spectra were recorded at 400 MHz on a jeol Eclipse+ 400 NMR spectrometer using Jeol Delta version 4.3.6 control and processing software.

3. MATERIALS20:

Name of the chemical

Batch and serial number

Manufactured by

Anthranilic acid

2-(H2N)C6H4CO2H

Mol.Wt 137.14

A89855

Sigma-Aldrich

Isoamyl nitrite

(CH3)2CHCH2CH2ONO

Mol. Wt 117.15

150495

Sigma-Aldrich

1,2- dimethoxyethane

CH3OCH2CH2OCH3

Mol. Wt 90.12

259527

Sigma-Aldrich

Furan

C4H4O

Mol. Wt 68.07

185922

Aldrich

Tetraphenyl cyclopentadienone

C29H20O

Mol. Wt 384.47

T25801

Aldrich

Anthracene

C14H10

Mol. Wt 178.23

A3885

Sigma-Aldrich

Sodium hydroxide

F24538

Sigma-Aldrich

Table 1: List of chemicals

4. Method:

Three methods were carried out to derive the benzyne. The methods are follows

Formation of benzyne and trapping with furan.

Formation of benzyne and trapping with tetraphenylcyclopentadienone.

Formation of benzyne and trapping with anthracene.

(A) Formation of benzyne and trapping with furan21:

Reaction 10: Formation of benzyne and trapping with furan.

Preparation of 1,4-dihydronaphthalene-1,4-endoxide

1, 2-Dimethoxyethane (10 ml), furan (10 ml) were taken in a 100 ml round bottomed flask, some boiling chip were added. The bottomed flask was fitted to reflux condenser and the solution was heated under steam. Meanwhile, two solutions were prepared in 25ml Erlenmeyer flask first one containing iso-amyl nitrate (4 ml) made up to 10 ml with 1,2-dimethoxyethane and second solution containing anthranilic acid (2.74 g) with 1,2-dimethoxyethane. 2ml of each solution was added by using separate Pasteur pipettes through the condenser to the round bottom flask under steam with 8-10 minutes intervals. After the solutions were fully added the solution turned to a dark orange colour. Then the mixture was refluxed for 30 min, on cooling this mixture to room temperature a dark brown mixture was precipitated out.

In the meantime sodium hydroxide (0.1 M) solution was prepared and added to dark brown mixture. The reaction mixture was then transferred to 100 ml separating funnel, organic layer was separated by extracting the product with 3-15 ml petroleum ether. The organic mixture was washed with 6-15 ml of distilled water and then organic solution was dried over magnesium sulphate and it was removed by suction. Finally the solution was decolourized with active charcoal powder (if the solution is very dark), and evaporated the filtrate on rotary evaporator. Crystalline slurry obtained was repurified by sublimation using ice cold petroleum ether.

Crystalline compound melting point was determined and the compound was analyses by IR, GC-MS and NMR.

1, 4-Dihydronaphthalene-1, 4-endoxide (0.432 g) was placed in 25 ml Erlenmeyer flask and dissolved in ethanol (10ml), concentrated hydrochloric acid was added to the solution and kept at room temperature for one hour. After one hour the reaction mixture was poured into 100 ml separating funnel, by adding diethyl ether (20 ml). Organic layer was separated by shaking the separating funnel. Then organic layer was dried over magnesium sulphate and the drying agent was removed by suction. Finally the solution was decolourized with active charcoal powder, and then evaporated the colourless solution on rotator evaporator to obtain crystalline slurry. Obtained crystalline slurry was repurified by sublimation using ice cold petroleum ether. The melting point of yield product was determined and final product was analysed by IR (Nujol), GC-MS and NMR.

(B) Formation of benzyne and trapping with tetracyclopetadienone13,29:

Synthesis of 1, 2, 3, 4- tetraphenylnaphthalene:

Reaction 11: Formation of benzyne and trapping with tetracyclopetadienone.

Tetraphenylcyclopentadienone (1 g), anthranilic acid (0.5 g), 1, 2-dimethoxyethane (12 ml) were placed in a 100ml round bottom flask fitted with an efficient reflux condenser and the solution was heated further under steam. On the other hand solution was prepared in a 20 ml disposable vial containing 0.6 ml of isopentyl nitrate ( isoamyl nitrate) dissolved in (5 ml) 1,2-dimethoxyethane and closed the cap the vial.

The reaction mixture was heated about 1400 C. When the solution started to boil, the solution isopentyl nitrate was added by using separate Pasteur pipettes through the condenser over a period of about 30 seconds. Then disposable vial rinsed with few drops of 1, 2-dimethoxyethane and added that to the reaction. The solution turned into orange colour when solutions were fully added, on the cooling this mixture to room temperature after that solution was transferred to beaker containing 50 ml water and 20 ml methanol, stirred the mixture well to break up the yellowish-orange precipitate.

Collected the solid by vacuum filtration and washed it with 20-30 ml of ice cold methanol, and then re-crystallised the product with 2-propanol by vacuum filtration, which gave a white powder. The melting point of the crystalline compound was determined and analysed by IR and GC-MS.

(C) Formation of benzyne and trapping with anthracene15:

Reaction 12: Formation of benzyne and trapping with anthracene.

Anthracene (2.60 g), isopentyl nitrate (2.62 ml) and 1, 2- dimethoxyethane (25 ml) were placed in a 250 ml round bottom flask and refluxed on an electric mantle. On the other hand a solution of anthranilic acid (3.40 g) in 1, 2-dimethoxyethane (15 ml) prepared and added drop-wise to the reaction mixture by using Pasteur pipette over the period of 30 minutes. The mixture was then cooled to room temperature and more isopentyl nitrate (2.62ml) dissolved in 1, 2-dimethoxyethane (5 ml) was added to it.

The gentle refluxing was continued; meanwhile another solution of anthranilic acid (3.40 g) in 1, 2-dimethoxyethane (10 ml) was added over a period of 15 minutes. The reaction mixture was then heated for further 15 minutes and industrial methylated spirit (10 ml) was added to it. The reaction mixture was transferred into a solution containing sodium hydroxide (3 g) in water (100 ml), which was turned to brown suspension and then thoroughly cooled in ice water and filter under suction. The residue was then washed with ice-cold methanol/water mixture (4:1 v/v) and transferred into a 100 ml round-bottom flask, which was then evaporated using rotary evaporator on a steam bath until the weight was constant. The crystals were then dried first by suction and then oven, which gave pale yellow crystalline solid.

The melting point of the crystalline compound was determined and the compound was analysed by IR (Nujol), and GC-MS.

5. Results and Discussion:

The obtained products from the above three procedures were analysed to know whether they are desired compounds or not by various analytical techniques. And these results are compared with that of the literature reference.

5.1. Melting point15,21:

Products

Product melting points range(0C)

Melting points range (0C)

1-Naphthalenol

94-98

94.5-96.5

1,2,3,4-Tetraphenylnaphthalene

200-201

199-201

Triptycene

222-225

225

Table 2: The products melting points

Percentage yield:

1-Naphthalenol (0.3738 g, 82.22%)

1, 2, 3, 4-Tetraphenylnaphthalene (0.33 g, 20.89%)

Triptycene (2.48 g, 39.43%).

5.2 IR spectra of the products26:

IR is a reliable means of identifying different functional groups present on the product by their characteristic vibration frequency, and comparing it with the groups present in the starting material.

Figure : IR Spectrum of 1, 4-dihydronaphthalene-1, 4-endoxide.

1, 4-dihydronaphthalene-1, 4-endoxide:

The FT-IR spectrum obtained for the compound, the peak at 2925.0 cm-1 which was due to the Nujol. This was further confirmed from the peaks 1456.1 cm-1 and 1377.2 cm-1. The peak at1728.0 cm-1 might be carbonyl group present in the compound (C-H stretch from aromatic ring). There are some more peaks obtained which may due to the presence of impurities or solvent.

Figure : IR spectrum of 1-napthalenol

1-Naphthalenol:

The FT-IR spectrum of the compound was obtained. The peak at 3306.58 cm-1 clearly showed OH (Phenol, Ar-OH) stretch, the peak was strong and broad. The peaks at 1598.63 cm-1 and 1598.63 cm-1 clearly showed C=C stretch, the peaks were variable. The peaks at 767.15 cm-1 710.53 cm-1 and 710.53 cm-1 clearly showed C-H bend (phenyl C6H5), peaks were strong. Prominent peaks were obtained for Nujol at 2924.11 cm-1, 2854.07 cm-1, 2954.11 cm-1, 1458.22 cm-1 and 1376.97 cm-1. There are other peaks obtained which may be due to the presence of impurities or solvent.

1, 2, 3, 4,-Tetraphenylnaphthalene:

Figure : IR spectrum of 1, 2, 3, 4-tetraphenylnaphthalene

According to the FT-IR spectrum of the compound the peaks obtained clearly showed aromatic C=C stretch at 1601.65 cm-1 and 1492.39 cm-1. The peaks at 744.79 cm-1 and 697.32 cm-1 clearly showed C-H bend (phenyl C6H5). The peaks at 2955.36 cm-1, 1459.28 cm-1 and 1376.67 cm-1 were because of Nujol.

5.3 GC-MS Spectra of the compounds27:

The gas chromatography-mass spectrometry is a combination of two techniques, where GC separates different components and mass spectra provides the structural fragmentation of the sample.

Figure : GC-MS of 1-naphthalenol

1-Naphthalenol:

Fragment

Mass-to-charge ratio(m/z)

C10OH8+

144

C9H7+

115

C7H5+

89

C5H3+

63

C5H2+

62

Table 3: Interpretation of GC-MS results of 1-Naphthalenol.

The full scan default mode with selected ions at m/z 62, 63, 89, 115, 144, was shown in above graph. As it can be seen in the figure, sample was well separated and the spectra showing last peak at 144(m/z).

From the above spectra, if we observe the molecular peak at 144 m/z and comparing it with the molecular weight of the desired product, and also verifying it with reference search ensured that this spectrum of the compound is very similar to the reference spectrum.

Hence, I conclude that the product is very similar to the desired product.

The full scan mode with selected ions at 77, 163, 177, 252, 276, 313, 339, 353, 389,414,432, was shown in above graph. As it can be seen in the figure, sample was well separated in a run time 25-26 minutes, and the spectrum showing most abundant peak at 432 m/z. But most of benzene compounds were eluted at same retention time which may be due to the handling procedures. The fragmentation of compound, it showed loss of phenyl rings from the attached naphthalene ring, and spectrum showing peaks at m/z 353, 276, 77 respectively. From the spectrum, if we see the molecular peak at 432 m/z, comparing it with the molecular weight of actual compound, and also verifying with reference that this spectrum of product is almost similar to reference spectrum. Hence, I conclude that the product is very similar to the desired product.

Triptycene:

Figure : GC-MS of triptycene.

Fragment

Mass-to-charge ratio(m/z)

C20H14+

254

C10H6+

126

C9H5+

113

C8H4+

100

Table 5: Interpretation of GC-MS results of Triptycene.

The full scan default mode with selected ions at m/z 100, 113,126 and 254 was shown in above graph. As it can be seen in the figure, sample was well separated and spectrum showing last peak at 254 m/z.

From the spectrum, we can see the molecular peak at 254 m/z and comparing it with the molecular weight of the desired compound, and verifying it with standard library search that this spectrum of the product is almost similar to reference spectrum. Hence, I conclude that obtained compound is very similar to the standard product.

5.4 Nuclear magnetic resonance spectra of compounds28:

1H NMR of 1- Naphthalenol

Figure : 1H NMR of 1- Naphthalenol

Figure :13C NMR for 1-Naphthalenol

The 1H NMR spectrum was obtained by using CDCl3 as a solvent. And obtained spectrum can explain the structure of the compound by showing chemical shifts of function groups.

In the above structure, 1-naphthalenol showed 6 different types of protons which are indicated as Ha, Hb, Hc, Hd, He, Hf, Hg, Hh and integration ratio is 1:1:1:1:1:3.

The peaks at 5.41 ppm, 6.72 ppm and 7.21 ppm, indicate Ha (singlet), Hb, Hc (doublet) protons respectively. The peak at 7.38 ppm with 3 integration values was because of Hd, Hg, Hf protons. These 3 protons were in same environment (doublet), and the rest of peaks at 7.73 ppm, 8.1 ppm was showed He, Hh protons respectively (doublet).

13C NMR of 1-Naphthalenol:

Carbon number

Chemical shift

C1

151.43

C2

134.82

C3

127.73

C4

126.49

C5

125.89

C6

125.31

C7

124.41

C8

121.59

C9

120.72

C10

108.67

Table 6: 13C NMR of 1-Naphthalenol

All the peaks were mostly similar and remaining peaks were found to be due to the impurities.

6. Conclusion:

Formation and trapping of benzyne has been successfully done by three different trapping agents which are fuaran, tetraphenylcyclopentadienone and anthracene with significant results.

In the first step, benzyne was trapped by furan and it may be obtained was 1, 4-dihydronaphthalene-1, 4-endoxide and it was confirmed by its IR spectrum. And then in additional step adduct obtained was 1-naphthalenol. The compound synthesised was crystalline in nature and dark brown in colour. The compound was confirmed by its melting point, IR, GC-MS and NMR spectrum compared with that literature values.

The benzyne was also trapped by using tetraphenylcyclopentadienone and the obtained adduct was 1, 2, 3, 4-tetraphenylnaphthalene, it was in crystalline in nature and yellow in orange (lemon yellow) colour. The compound was confirmed by its melting point, IR, GC-MS spectrum compared with that of standards.

Similarly the benzyne was also trapped by using anthracene and the obtained adduct was triptycen. The compound was orange yellow in colour and crystalline in nature. It was also confirmed by its melting point, GC-MS spectrum compared with that of the literature values.

7. Further work:

Positive results were received in above three methods, even though it may not be enough to describe the formation and trapping of benzyne with dienes. Not only the above mentioned trapping agents there are other trapping agents such as nitrile oxides can be used as trapping agents to produce heterocycles.

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